PMID- 18453553
OWN - NLM
STAT- MEDLINE
DCOM- 20080725
LR  - 20211020
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 24
IP  - 13
DP  - 2008 Jul 1
TI  - High-performance hardware implementation of a parallel database search engine for 
      real-time peptide mass fingerprinting.
PG  - 1498-502
LID - 10.1093/bioinformatics/btn216 [doi]
AB  - Peptide mass fingerprinting (PMF) is a method for protein identification in which 
      a protein is fragmented by a defined cleavage protocol (usually proteolysis with 
      trypsin), and the masses of these products constitute a 'fingerprint' that can be 
      searched against theoretical fingerprints of all known proteins. In the first 
      stage of PMF, the raw mass spectrometric data are processed to generate a peptide 
      mass list. In the second stage this protein fingerprint is used to search a 
      database of known proteins for the best protein match. Although current software 
      solutions can typically deliver a match in a relatively short time, a system that 
      can find a match in real time could change the way in which PMF is deployed and 
      presented. In a paper published earlier we presented a hardware design of a raw 
      mass spectra processor that, when implemented in Field Programmable Gate Array 
      (FPGA) hardware, achieves almost 170-fold speed gain relative to a conventional 
      software implementation running on a dual processor server. In this article we 
      present a complementary hardware realization of a parallel database search engine 
      that, when running on a Xilinx Virtex 2 FPGA at 100 MHz, delivers 1800-fold 
      speed-up compared with an equivalent C software routine, running on a 3.06 GHz 
      Xeon workstation. The inherent scalability of the design means that processing 
      speed can be multiplied by deploying the design on multiple FPGAs. The database 
      search processor and the mass spectra processor, running on a reconfigurable 
      computing platform, provide a complete real-time PMF protein identification 
      solution.
FAU - Bogdan, Istvan A
AU  - Bogdan IA
AD  - Department of Automatic Control & Systems Engineering, The University of 
      Sheffield, Mappin Street, Sheffield S1 3JD, UK.
FAU - Rivers, Jenny
AU  - Rivers J
FAU - Beynon, Robert J
AU  - Beynon RJ
FAU - Coca, Daniel
AU  - Coca D
LA  - eng
GR  - BB/F004745/1/BB_/Biotechnology and Biological Sciences Research Council/United 
      Kingdom
GR  - BB/F004893/1/BB_/Biotechnology and Biological Sciences Research Council/United 
      Kingdom
GR  - BBS/B/16402/BB_/Biotechnology and Biological Sciences Research Council/United 
      Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20080503
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - Computer Systems
MH  - Database Management Systems/*instrumentation
MH  - *Databases, Factual
MH  - Equipment Design
MH  - Equipment Failure Analysis
MH  - Information Storage and Retrieval/*methods
MH  - Mass Spectrometry/*instrumentation
MH  - Peptide Mapping/*instrumentation
PMC - PMC3133936
EDAT- 2008/05/06 09:00
MHDA- 2008/07/26 09:00
PMCR- 2009/07/01
CRDT- 2008/05/06 09:00
PHST- 2008/05/06 09:00 [pubmed]
PHST- 2008/07/26 09:00 [medline]
PHST- 2008/05/06 09:00 [entrez]
PHST- 2009/07/01 00:00 [pmc-release]
AID - btn216 [pii]
AID - 10.1093/bioinformatics/btn216 [doi]
PST - ppublish
SO  - Bioinformatics. 2008 Jul 1;24(13):1498-502. doi: 10.1093/bioinformatics/btn216. 
      Epub 2008 May 3.